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Coexpression cluster:C2427: Difference between revisions

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|tf_chipseq_enrich=FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353450159034781
|tf_chipseq_enrich=FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353450159034781
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}}
}}

Revision as of 15:29, 26 November 2012


Full id: C2427_CD14_Neutrophils_CD8_CD4_Peripheral_Monocytederived_Natural



Phase1 CAGE Peaks

Hg19::chr17:62499151..62499235,-p@chr17:62499151..62499235
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Hg19::chr17:62499334..62499416,-p4@DDX5
Hg19::chr17:62500904..62500938,-p@chr17:62500904..62500938
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Hg19::chr17:62500949..62500966,-p@chr17:62500949..62500966
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Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
classical monocyte3.92e-2342
CD14-positive, CD16-negative classical monocyte3.92e-2342
leukocyte4.36e-23136
defensive cell1.92e-2148
phagocyte1.92e-2148
nongranular leukocyte1.52e-20115
hematopoietic lineage restricted progenitor cell1.78e-19120
hematopoietic stem cell3.09e-18168
angioblastic mesenchymal cell3.09e-18168
hematopoietic oligopotent progenitor cell2.53e-17161
hematopoietic multipotent progenitor cell2.53e-17161
hematopoietic cell5.46e-16177
myeloid leukocyte8.29e-1672
macrophage dendritic cell progenitor8.36e-1661
monopoietic cell2.98e-1559
monocyte2.98e-1559
monoblast2.98e-1559
promonocyte2.98e-1559
granulocyte monocyte progenitor cell4.49e-1467
myeloid lineage restricted progenitor cell9.48e-1466
myeloid cell1.26e-11108
common myeloid progenitor1.26e-11108
stuff accumulating cell9.59e-1187
mesenchymal cell4.66e-08354
connective tissue cell5.74e-07361
Uber Anatomy
Ontology termp-valuen
bone marrow5.13e-1176
bone element6.29e-1082
hematopoietic system6.92e-1098
blood island6.92e-1098
hemolymphoid system2.64e-08108
immune system6.77e-0893
skeletal element1.07e-0790
skeletal system1.73e-07100


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOXA2#3170212.31523187633260.009361916285467240.0353450159034781



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.